Starting phenix.real_space_refine on Fri Sep 19 04:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psz_17865/09_2025/8psz_17865_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psz_17865/09_2025/8psz_17865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psz_17865/09_2025/8psz_17865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psz_17865/09_2025/8psz_17865.map" model { file = "/net/cci-nas-00/data/ceres_data/8psz_17865/09_2025/8psz_17865_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psz_17865/09_2025/8psz_17865_trim.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 56 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7221 2.51 5 N 2077 2.21 5 O 2481 1.98 5 H 11195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23098 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6653 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 bond proxies already assigned to first conformer: 7960 Chain: "C" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6652 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 22, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "S" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 422 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 411 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'A0I': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 46.840 53.436 18.382 1.00 20.80 S ATOM 4474 SG CYS A 282 44.558 52.018 15.484 1.00 21.12 S ATOM 18191 SG CYS C 233 23.667 63.533 108.687 1.00 68.90 S ATOM 18215 SG CYS C 235 23.744 64.404 104.935 1.00 63.55 S ATOM 16857 SG CYS C 146 12.028 72.706 88.850 1.00 71.81 S ATOM 17045 SG CYS C 159 13.000 75.499 90.912 1.00 66.96 S ATOM 17101 SG CYS C 163 15.366 72.687 90.646 1.00 60.91 S ATOM 17111 SG CYS C 164 14.711 75.039 87.428 1.00 64.71 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASP B 213 " occ=0.50 ... (22 atoms not shown) pdb=" HB3BASP B 213 " occ=0.50 residue: pdb=" N ATYR B 393 " occ=0.60 ... (40 atoms not shown) pdb=" HH BTYR B 393 " occ=0.40 Time building chain proxies: 5.50, per 1000 atoms: 0.24 Number of scatterers: 23098 At special positions: 0 Unit cell: (92.4, 109.2, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 56 15.00 Mg 2 11.99 O 2481 8.00 N 2077 7.00 C 7221 6.00 H 11195 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 877.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 9 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 42.4% alpha, 13.9% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.878A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.523A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.967A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.555A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.501A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.648A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.646A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.728A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.972A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.035A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.736A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 removed outlier: 3.549A pdb=" N GLY C 165 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.627A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.540A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.302A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.302A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.129A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.779A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.623A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11163 1.03 - 1.23: 52 1.23 - 1.42: 5191 1.42 - 1.62: 6842 1.62 - 1.81: 89 Bond restraints: 23337 Sorted by residual: bond pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 1.731 1.618 0.113 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C PRO C 234 " pdb=" O PRO C 234 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.30e-02 5.92e+03 1.98e+01 bond pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 1.701 1.641 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O3 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.662 1.603 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" N4 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.691 1.642 0.049 2.00e-02 2.50e+03 5.88e+00 ... (remaining 23332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 41535 1.62 - 3.25: 539 3.25 - 4.87: 46 4.87 - 6.50: 2 6.50 - 8.12: 1 Bond angle restraints: 42123 Sorted by residual: angle pdb=" O6 A0I B 601 " pdb=" P2 A0I B 601 " pdb=" O7 A0I B 601 " ideal model delta sigma weight residual 112.52 104.40 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" N PRO C 234 " pdb=" CA PRO C 234 " pdb=" CB PRO C 234 " ideal model delta sigma weight residual 103.25 100.43 2.82 1.05e+00 9.07e-01 7.19e+00 angle pdb=" C LYS A 163 " pdb=" CA LYS A 163 " pdb=" CB LYS A 163 " ideal model delta sigma weight residual 110.42 115.61 -5.19 1.99e+00 2.53e-01 6.79e+00 angle pdb=" CA PRO C 234 " pdb=" C PRO C 234 " pdb=" O PRO C 234 " ideal model delta sigma weight residual 120.60 116.81 3.79 1.82e+00 3.02e-01 4.33e+00 angle pdb=" N ASP C 345 " pdb=" CA ASP C 345 " pdb=" C ASP C 345 " ideal model delta sigma weight residual 114.75 112.49 2.26 1.26e+00 6.30e-01 3.22e+00 ... (remaining 42118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9721 17.80 - 35.60: 836 35.60 - 53.41: 342 53.41 - 71.21: 120 71.21 - 89.01: 29 Dihedral angle restraints: 11048 sinusoidal: 6454 harmonic: 4594 Sorted by residual: dihedral pdb=" CD ARG B 176 " pdb=" NE ARG B 176 " pdb=" CZ ARG B 176 " pdb=" NH1 ARG B 176 " ideal model delta sinusoidal sigma weight residual 0.00 41.02 -41.02 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA SER B 286 " pdb=" C SER B 286 " pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 11045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1586 0.044 - 0.088: 227 0.088 - 0.132: 87 0.132 - 0.176: 0 0.176 - 0.220: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" C7 A0I B 601 " pdb=" C6 A0I B 601 " pdb=" C8 A0I B 601 " pdb=" O12 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.59 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL C 221 " pdb=" N VAL C 221 " pdb=" C VAL C 221 " pdb=" CB VAL C 221 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL A 252 " pdb=" N VAL A 252 " pdb=" C VAL A 252 " pdb=" CB VAL A 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1898 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 176 " 0.749 9.50e-02 1.11e+02 2.50e-01 6.59e+01 pdb=" NE ARG B 176 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 176 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 176 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 176 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 176 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG B 176 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B 176 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 176 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 3 " -0.022 2.00e-02 2.50e+03 9.08e-03 2.68e+00 pdb=" N9 A V 3 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 3 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 3 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A V 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 162 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.019 5.00e-02 4.00e+02 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 898 2.16 - 2.77: 43029 2.77 - 3.38: 65847 3.38 - 3.99: 89220 3.99 - 4.60: 135252 Nonbonded interactions: 334246 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.549 2.450 nonbonded pdb=" H GLY A 239 " pdb=" O ALA A 251 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASN B 397 " pdb=" HG1 THR B 399 " model vdw 1.590 2.450 nonbonded pdb=" H GLY C 85 " pdb=" OD1 ASP C 110 " model vdw 1.630 2.450 nonbonded pdb=" HG1 THR B 103 " pdb=" O ILE B 125 " model vdw 1.631 2.450 ... (remaining 334241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 5 through 17) selection = (chain 'S' and (resid 28 through 34 or resid 36 through 40)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 33.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 12154 Z= 0.138 Angle : 0.506 9.351 16675 Z= 0.257 Chirality : 0.037 0.220 1901 Planarity : 0.008 0.321 1951 Dihedral : 17.754 89.008 4872 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.06 % Allowed : 16.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.23), residues: 1351 helix: 1.65 (0.23), residues: 525 sheet: 0.20 (0.40), residues: 148 loop : -0.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.012 0.001 TYR C 315 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00281 (12142) covalent geometry : angle 0.49343 (16666) hydrogen bonds : bond 0.12888 ( 514) hydrogen bonds : angle 5.58584 ( 1410) metal coordination : bond 0.00840 ( 12) metal coordination : angle 4.80964 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8594 (mttt) cc_final: 0.8364 (mttp) REVERT: A 332 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: B 282 ASP cc_start: 0.8477 (p0) cc_final: 0.8276 (p0) REVERT: B 480 GLU cc_start: 0.7593 (tt0) cc_final: 0.7385 (tt0) REVERT: C 77 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (ptt90) REVERT: C 89 GLU cc_start: 0.7603 (mp0) cc_final: 0.7392 (mp0) REVERT: C 109 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7065 (mp10) REVERT: C 348 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7637 (mppt) REVERT: C 351 ILE cc_start: 0.7809 (mm) cc_final: 0.7532 (mm) REVERT: C 413 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7524 (mtmt) REVERT: C 427 LYS cc_start: 0.7300 (ttmt) cc_final: 0.7088 (tttm) outliers start: 24 outliers final: 9 residues processed: 194 average time/residue: 1.9750 time to fit residues: 404.8051 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 200 GLN B 44 ASN C 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.086732 restraints weight = 45586.127| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.68 r_work: 0.2826 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12154 Z= 0.113 Angle : 0.498 5.350 16675 Z= 0.261 Chirality : 0.037 0.140 1901 Planarity : 0.005 0.075 1951 Dihedral : 13.020 73.565 2316 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.46 % Allowed : 16.38 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.23), residues: 1351 helix: 1.89 (0.23), residues: 530 sheet: 0.03 (0.40), residues: 145 loop : 0.01 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.013 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00245 (12142) covalent geometry : angle 0.49443 (16666) hydrogen bonds : bond 0.04430 ( 514) hydrogen bonds : angle 4.58918 ( 1410) metal coordination : bond 0.00619 ( 12) metal coordination : angle 2.63423 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.6471 (m110) cc_final: 0.6175 (m110) REVERT: A 279 LYS cc_start: 0.8705 (mttt) cc_final: 0.8359 (mttp) REVERT: B 480 GLU cc_start: 0.7809 (tt0) cc_final: 0.7454 (tt0) REVERT: C 77 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8691 (ptt90) REVERT: C 89 GLU cc_start: 0.7412 (mp0) cc_final: 0.7098 (mp0) REVERT: C 109 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7051 (mp10) REVERT: C 196 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6577 (mt-10) REVERT: C 348 LYS cc_start: 0.8119 (mmtp) cc_final: 0.7483 (mppt) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 2.0579 time to fit residues: 310.5839 Evaluate side-chains 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.083672 restraints weight = 50845.410| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.78 r_work: 0.2770 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12154 Z= 0.184 Angle : 0.534 5.410 16675 Z= 0.281 Chirality : 0.039 0.139 1901 Planarity : 0.005 0.060 1951 Dihedral : 13.061 73.602 2311 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.89 % Allowed : 16.04 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.22), residues: 1351 helix: 1.74 (0.23), residues: 530 sheet: -0.08 (0.40), residues: 145 loop : -0.11 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 83 TYR 0.017 0.002 TYR A 403 PHE 0.016 0.002 PHE C 44 TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00413 (12142) covalent geometry : angle 0.53033 (16666) hydrogen bonds : bond 0.05189 ( 514) hydrogen bonds : angle 4.59824 ( 1410) metal coordination : bond 0.00708 ( 12) metal coordination : angle 2.88039 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8704 (mttt) cc_final: 0.8424 (mttp) REVERT: B 53 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7590 (pptt) REVERT: B 480 GLU cc_start: 0.7919 (tt0) cc_final: 0.7569 (tt0) REVERT: C 89 GLU cc_start: 0.7385 (mp0) cc_final: 0.7168 (mp0) REVERT: C 109 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7087 (mp10) REVERT: C 170 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6782 (mtpp) REVERT: C 196 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6479 (mt-10) REVERT: C 348 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7532 (mppt) outliers start: 22 outliers final: 13 residues processed: 136 average time/residue: 2.1680 time to fit residues: 309.9487 Evaluate side-chains 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.084640 restraints weight = 48409.573| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.70 r_work: 0.2792 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12154 Z= 0.146 Angle : 0.506 5.527 16675 Z= 0.266 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.054 1951 Dihedral : 12.836 73.601 2307 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.54 % Allowed : 16.12 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.22), residues: 1351 helix: 1.76 (0.23), residues: 530 sheet: -0.14 (0.40), residues: 145 loop : -0.16 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.015 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00323 (12142) covalent geometry : angle 0.50254 (16666) hydrogen bonds : bond 0.04629 ( 514) hydrogen bonds : angle 4.48285 ( 1410) metal coordination : bond 0.00604 ( 12) metal coordination : angle 2.59550 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8681 (mttt) cc_final: 0.8402 (mttp) REVERT: B 53 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7510 (pptt) REVERT: B 180 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.9014 (t) REVERT: B 480 GLU cc_start: 0.7908 (tt0) cc_final: 0.7586 (tt0) REVERT: B 495 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7427 (tmmt) REVERT: C 89 GLU cc_start: 0.7315 (mp0) cc_final: 0.7011 (mp0) REVERT: C 109 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7095 (mp10) REVERT: C 170 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6737 (mtpt) REVERT: C 196 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: C 348 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7513 (mppt) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 2.0945 time to fit residues: 289.8333 Evaluate side-chains 129 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.084260 restraints weight = 56054.740| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.86 r_work: 0.2780 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12154 Z= 0.144 Angle : 0.501 5.559 16675 Z= 0.263 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.052 1951 Dihedral : 12.755 73.584 2302 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.80 % Allowed : 15.78 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.22), residues: 1351 helix: 1.77 (0.23), residues: 530 sheet: -0.15 (0.40), residues: 145 loop : -0.16 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 83 TYR 0.015 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00322 (12142) covalent geometry : angle 0.49779 (16666) hydrogen bonds : bond 0.04598 ( 514) hydrogen bonds : angle 4.45044 ( 1410) metal coordination : bond 0.00568 ( 12) metal coordination : angle 2.54915 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8687 (mttt) cc_final: 0.8410 (mttp) REVERT: B 53 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7516 (pptt) REVERT: B 480 GLU cc_start: 0.7901 (tt0) cc_final: 0.7599 (tt0) REVERT: B 495 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7464 (tmmt) REVERT: C 89 GLU cc_start: 0.7309 (mp0) cc_final: 0.7031 (mp0) REVERT: C 109 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7094 (mp10) REVERT: C 170 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6793 (mtpt) REVERT: C 196 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6526 (mt-10) REVERT: C 348 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7526 (mppt) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 2.0908 time to fit residues: 292.6796 Evaluate side-chains 129 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN C 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.083360 restraints weight = 49829.931| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.74 r_work: 0.2771 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12154 Z= 0.192 Angle : 0.539 5.735 16675 Z= 0.284 Chirality : 0.039 0.139 1901 Planarity : 0.005 0.051 1951 Dihedral : 12.870 73.596 2302 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.54 % Allowed : 15.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.22), residues: 1351 helix: 1.62 (0.22), residues: 530 sheet: -0.20 (0.41), residues: 133 loop : -0.22 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 83 TYR 0.017 0.002 TYR A 403 PHE 0.016 0.002 PHE C 44 TRP 0.010 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00431 (12142) covalent geometry : angle 0.53543 (16666) hydrogen bonds : bond 0.05101 ( 514) hydrogen bonds : angle 4.54911 ( 1410) metal coordination : bond 0.00775 ( 12) metal coordination : angle 2.83903 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8679 (mttt) cc_final: 0.8400 (mttp) REVERT: B 53 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7534 (pptt) REVERT: B 159 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.8932 (mt) REVERT: B 495 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7431 (tmmt) REVERT: C 109 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7078 (mp10) REVERT: C 196 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: C 348 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7598 (mppt) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 1.8091 time to fit residues: 249.0063 Evaluate side-chains 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.084336 restraints weight = 43603.270| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.64 r_work: 0.2787 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12154 Z= 0.178 Angle : 0.532 5.736 16675 Z= 0.280 Chirality : 0.038 0.138 1901 Planarity : 0.005 0.062 1951 Dihedral : 12.836 73.568 2302 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.63 % Allowed : 15.95 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.22), residues: 1351 helix: 1.60 (0.22), residues: 531 sheet: -0.23 (0.39), residues: 145 loop : -0.20 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 83 TYR 0.015 0.002 TYR A 403 PHE 0.014 0.001 PHE C 44 TRP 0.010 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00400 (12142) covalent geometry : angle 0.52815 (16666) hydrogen bonds : bond 0.04931 ( 514) hydrogen bonds : angle 4.51180 ( 1410) metal coordination : bond 0.00758 ( 12) metal coordination : angle 2.66756 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8671 (mttt) cc_final: 0.8394 (mttp) REVERT: B 28 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: B 159 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.8929 (mt) REVERT: B 495 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7461 (tmmt) REVERT: C 109 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7081 (mp10) REVERT: C 196 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: C 348 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7597 (mppt) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 2.1240 time to fit residues: 291.5621 Evaluate side-chains 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.082891 restraints weight = 51249.115| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.78 r_work: 0.2761 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12154 Z= 0.217 Angle : 0.563 5.749 16675 Z= 0.297 Chirality : 0.040 0.138 1901 Planarity : 0.005 0.079 1951 Dihedral : 12.949 73.609 2302 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.54 % Allowed : 16.04 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.22), residues: 1351 helix: 1.47 (0.22), residues: 530 sheet: -0.40 (0.40), residues: 138 loop : -0.25 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 83 TYR 0.017 0.002 TYR A 403 PHE 0.017 0.002 PHE C 44 TRP 0.011 0.001 TRP A 346 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00489 (12142) covalent geometry : angle 0.55828 (16666) hydrogen bonds : bond 0.05365 ( 514) hydrogen bonds : angle 4.61793 ( 1410) metal coordination : bond 0.00864 ( 12) metal coordination : angle 3.03146 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8686 (mttt) cc_final: 0.8402 (mttp) REVERT: B 159 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.8942 (mt) REVERT: B 495 LYS cc_start: 0.7742 (ttpp) cc_final: 0.7532 (tmmt) REVERT: C 109 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7090 (mp10) REVERT: C 196 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: C 348 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7641 (mppt) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 2.2657 time to fit residues: 305.5558 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.085567 restraints weight = 50648.870| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.78 r_work: 0.2806 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12154 Z= 0.114 Angle : 0.488 5.483 16675 Z= 0.255 Chirality : 0.037 0.138 1901 Planarity : 0.005 0.075 1951 Dihedral : 12.693 73.584 2302 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.37 % Allowed : 16.21 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.22), residues: 1351 helix: 1.78 (0.23), residues: 531 sheet: -0.24 (0.40), residues: 145 loop : -0.15 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 83 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 175 TRP 0.007 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00253 (12142) covalent geometry : angle 0.48523 (16666) hydrogen bonds : bond 0.04206 ( 514) hydrogen bonds : angle 4.36212 ( 1410) metal coordination : bond 0.00537 ( 12) metal coordination : angle 2.29405 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8069 (t70) cc_final: 0.7844 (t0) REVERT: B 159 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.8933 (mt) REVERT: B 180 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.9008 (t) REVERT: C 28 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.6043 (t-90) REVERT: C 109 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7018 (mp10) REVERT: C 348 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7585 (mppt) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 2.0712 time to fit residues: 280.2472 Evaluate side-chains 129 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 26 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.085770 restraints weight = 41834.614| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.61 r_work: 0.2811 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12154 Z= 0.135 Angle : 0.500 5.457 16675 Z= 0.262 Chirality : 0.037 0.137 1901 Planarity : 0.005 0.077 1951 Dihedral : 12.691 73.580 2302 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.20 % Allowed : 16.55 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.22), residues: 1351 helix: 1.77 (0.23), residues: 531 sheet: -0.25 (0.40), residues: 145 loop : -0.13 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 83 TYR 0.013 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00301 (12142) covalent geometry : angle 0.49730 (16666) hydrogen bonds : bond 0.04429 ( 514) hydrogen bonds : angle 4.37951 ( 1410) metal coordination : bond 0.00560 ( 12) metal coordination : angle 2.36663 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8215 (t70) cc_final: 0.8002 (t0) REVERT: B 159 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.8934 (mt) REVERT: B 180 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.9000 (t) REVERT: C 28 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6060 (t-90) REVERT: C 109 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7069 (mp10) REVERT: C 348 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7632 (mppt) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 2.0677 time to fit residues: 268.7440 Evaluate side-chains 127 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086833 restraints weight = 45811.020| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.69 r_work: 0.2831 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12154 Z= 0.103 Angle : 0.475 5.321 16675 Z= 0.248 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.076 1951 Dihedral : 12.553 73.555 2302 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.94 % Allowed : 16.81 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.23), residues: 1351 helix: 1.93 (0.23), residues: 531 sheet: -0.09 (0.41), residues: 143 loop : -0.08 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 83 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 175 TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00228 (12142) covalent geometry : angle 0.47233 (16666) hydrogen bonds : bond 0.03907 ( 514) hydrogen bonds : angle 4.24462 ( 1410) metal coordination : bond 0.00501 ( 12) metal coordination : angle 2.05033 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10896.67 seconds wall clock time: 184 minutes 40.34 seconds (11080.34 seconds total)